[gmx-users] corrupt trr file?

[David van der Spoel]

Samantha Kaye wrote:
> I tried to generate my continuation file from 4500 using tpbconv. Any reason the shouldn't work? Do I need to truncate the trr file specifically?
> 
if you don't have velocities it won't work. try 4000, or check first 
where you do have velocities using gmxcheck.
> 
> 
> 
> In message <44C51F84.5090809 at xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
>> Samantha Kaye wrote:
>>> But the first file can't be successfully gmxcheck-ed, I get the precision error mentioned below.
>> ok, I see. You will have to truncate it after 4500 ps using trjconv -e 
>> or trjconv -trunc
>>
>>>
>>> In message <44C504B8.2040101 at xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
>>>
>>>> Samantha Kaye wrote:
>>>>
>>>>> Yes using trjcat. It returns a magic number error.
>>>> could this by chance be run on a 64 bit powerpc?
>>>>
>>>> If the two original files can be gmxcheck-ed then the catted file should 
>>>> be fine too.
>>>>
>>>>
>>>>> In message <44C4CA58.5080209 at xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
>>>>>
>>>>>
>>>>>> Samantha Kaye wrote:
>>>>>>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Whenever I try to make a continuation file for my simulation I can generate a tpr file using tpbconv but I can't cat the ouput files together afterwards.
>>>>>>>
>>>>>> did you use trjcat ?
>>>>>>
>>>>>>
>>>>>>
>>>>>>> When I run ">gmxcheck -f closed1122_unrest.trr" on the first trr file I get the following:
>>>>>>>
>>>>>>>
>>>>>>> Checking file closed1122_unrest.trr
>>>>>>> trn version: GMX_trn_file (single precision)
>>>>>>> Reading frame       0 time    0.000
>>>>>>> # Atoms  189376
>>>>>>> Reading frame     910 time 4550.000   -------------------------------------------------------
>>>>>>> Program gmxcheck, VERSION 3.3
>>>>>>> Source code file: trnio.c, line: 66
>>>>>>>
>>>>>>> File input/output error:
>>>>>>> Can not determine precision of trn file
>>>>>>> -------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> I've tried generating the continuation file from an earlier frame but have the same problem always at frame 910.
>>>>>>>
>>>>>>> The file is over 2gb but as tpbconv runs without a problem I don't think that's the problem.
>>>>>>>
>>>>>>> Any suggestions?
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> David.
>>>>>> ________________________________________________________________________
>>>>>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>>>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>>>> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>>>>>> phone:	46 18 471 4205		fax: 46 18 511 755
>>>>>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
>>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>>>> www interface or send it to gmx-users-request at gromacs.org.
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>>>>>>
>>>>>
>>>> -- 
>>>> David.
>>>> ________________________________________________________________________
>>>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>>>> phone:	46 18 471 4205		fax: 46 18 511 755
>>>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>> www interface or send it to gmx-users-request at gromacs.org.
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>>>>
>>>
>>
>> -- 
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>> phone:	46 18 471 4205		fax: 46 18 511 755
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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